Tweet
phylogenetic tree construction
Hi,
I have isolated
I have isolated
-
Last edited by juannajuann; 12-31-2013, 06:46 AM. -
Basically, you can construct a phylogenetic tree from any set of related sequences. However, to construct a robust tree, you need to have all the relevant taxa well (evenly) represented, as well as a well thought-out outgroup. Maybe your best bet would be to simply take 16S/other marker genes and add it/them to some pre-made alignment/s?Originally posted by juannajuann View PostHi,
I have isolated 9 soil bacteria and sent for sequencing. I had identified them using BLASTn. The results showed that 5 of them belong to genus Bacillus, 2 strains belong to genus Serratia , 1 strain is genus Pseudomonas and 1 strain belong to genus Escherichia.
Now, I would like to construct phylogenetic tree. However, I not sure how to do it.
So, can I just construct a phylogenetic tree that only consists 9 strains of my study bacteria samples?
Or do I need to construct a phylogenetic tree that consists of my study isolated bacteria together with some related bacteria species??
Please help me to remove all my doubt... Thanks.Last edited by rhinoceros; 07-31-2013, 04:34 AM.savetherhino.org -
Originally posted by rhinoceros View Post
So, you mean the phylogentic tree include my bacteria strain and some related species...
It is the phylogenetic somehow look like this, just for example
[IMG]
[/IMG]
Sorry, I am new in this thing. So, I am not sure how to do it.Comment
-
What is the question you want to answer with your tree? If it's the taxonomic placement of your samples, then obviously constructing a tree that includes only your samples will not take you very far. For precise taxonomic placement, you really should just add your sequences to some pre-made alignment..Originally posted by juannajuann View Postsavetherhino.orgComment
-
There is some journal that construct phylogenetic tree using the isolated strains only...
for example,
............Well, basically I just want to study the evolutionary relationship among the isolated bacteria. I just not very sure the best way to construct the phylogenetic tree.Comment
-
You can use just your isolated samples if you are only interested in the relationships amongst them. If you wish to generate a rooted tree, then you will need an appropriate outgroup (preferable several sequences, not just one arbitrary one).
But you can generate unrooted cladograms with the sequences you have.
A free suite of tools like PHYLIP will let you explore using distance, ML and Parsimony methods. There are other free tools to explore Bayesian methods or alternate models as well.
Be wary of misinterpreting branch lengths though, if you are not able to flesh out the data set with additional related species.Michael Black, Ph.D.
ScitoVation LLC. RTP, N.C.Comment
-
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM -
With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.
Introduction
Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...05-22-2026, 06:42 AM
Comment